Demonstrator: Napari-KICS

Speaker: Arne Ludwig

Date: October 27^th 2022, 1 p.m. – 2 p.m.

Location: ScaDS.AI Living Lab (APB-1020), Andreas-Pfitzmann-Bau (APB), Nöthnitzer Str. 46, 01187 Dresden, Germany

Know your chromosome sizes: a guide to karyotype-based validation of de novo assemblies.

Check out this application on Github.

Chromosome-scale genome assembly is affected by scaffolding errors and may yield incorrect chromosome sizes. Today, we present Napari-KICS, a semi-automated and cost-efficient approach for examining the validity of the assembly by estimating relative chromosome sizes from the respective karyotype images. The method employs threshold-based image segmentation and uses the extracted chromosome areas as proxies for the actual chromosome sizes. The suitability of the approach is confirmed by a strong correlation between area and DNA content evaluated on karyotype images of varied species and achieving a 6 Mb chromosome size error on a reference human karyotype dataset.

Hands-On Demonstrator Series

In the ScaDS.AI Living Lab Hands-On Demonstrator Series, we showcase the latest accomplishments, discoveries, improvements and educational tools of the ScaDS.AI team in the field of AI, Big Data and Data Science. The introductory talk, Q&A and hands-on session will provide you with a chance to familiarize yourself with the demonstrator. 

Find out more about our Hands-on Demonstrator Series!